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epiNEM

Epistatic Nested Effects Models - https://doi.org/10.1371/journal.pcbi.1005496 - https://bioconductor.org/packages/epiNEM/

https://github.com/cbg-ethz/epinem

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    Found codemeta.json file
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    Found .zenodo.json file
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    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
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    Committers with academic emails
    2 of 10 committers (20.0%) from academic institutions
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    Institutional organization owner
    Organization cbg-ethz has institutional domain (www.bsse.ethz.ch)
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (5.8%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene genomics transcriptomics metabolomics proteomics annotation-agnostic count exon human
Last synced: 9 months ago · JSON representation

Repository

Epistatic Nested Effects Models - https://doi.org/10.1371/journal.pcbi.1005496 - https://bioconductor.org/packages/epiNEM/

Basic Info
  • Host: GitHub
  • Owner: cbg-ethz
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 11.9 MB
Statistics
  • Stars: 1
  • Watchers: 5
  • Forks: 1
  • Open Issues: 0
  • Releases: 1
Created over 10 years ago · Last pushed about 1 year ago
Metadata Files
Readme

README.md

epiNEM

EpiNEM is a direct extension of the NEM framework. epiNEM focuses on the epistasis between three S-genes, namely two parents and one child. Epistasis occurs, when the single effects of the two parents do not explain their combined effect on the child. EpiNEM models this epistasis with five Boolean logical gates for a triplet A->C, B->C.

  • A or B, OR: A has an effect on C, B has an effect on C, A+B has an effect on C
  • A and B, AND: A has no effect on C, B has no effect on C, A+B has an effect on C
  • (not A and B) or (A and not B), XOR: A has an effect on C, B has an effect on C, A+B has no effect on C
  • not A and B, A masks the effect of B: A has no effect on C, B has an effect on C, A+B has no effect on C
  • A and not B, B masks the effect of A: A has an effect on C, B has no effect on C, A+B has no effect on C

Install:

```{r} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("epiNEM") ```

Most recent (devel) version:

```r install.packages("devtools")

library(devtools)

install_github("cbg-ethz/epiNEM")

library(epiNEM) ```

Check out the vignette for working examples and the reproduction of the publication.

r vignette(package="epiNEM")

Toy example:

```r data <- matrix(sample(c(0,1), 100*4, replace = T), 100, 4)

colnames(data) <- c("A", "A.B", "B", "C")

rownames(data) <- paste("E", 1:100, sep = "_")

res <- epiNEM(data, method = "exhaustive")

plot(res) ```

References

Pirkl M, Diekmann M, van der Wees M, Beerenwinkel N, Frhlich H, Markowetz F (2017). "Inferring modulators of genetic interactions with epistatic nested effects models." PLOS Computational Biology, 13, 1-18. doi: 10.1371/journal.pcbi.1005496.

Owner

  • Name: Computational Biology Group (CBG)
  • Login: cbg-ethz
  • Kind: organization
  • Location: Basel, Switzerland

Beerenwinkel Lab at ETH Zurich

GitHub Events

Total
  • Push event: 3
Last Year
  • Push event: 3

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 79
  • Total Committers: 10
  • Avg Commits per committer: 7.9
  • Development Distribution Score (DDS): 0.595
Past Year
  • Commits: 5
  • Committers: 2
  • Avg Commits per committer: 2.5
  • Development Distribution Score (DDS): 0.2
Top Committers
Name Email Commits
mpirkl m****l@b****h 32
Nitesh Turaga n****a@g****m 14
J Wokaty j****y@s****u 12
mpirkl m****l@y****e 11
vobencha v****a@g****m 2
Hervé Pagès h****s@f****g 2
vobencha v****n@r****g 2
Herve Pages h****s@f****g 2
lshep l****d@r****g 1
Martin Morgan m****n@f****g 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 2 roswellpark.org: 2 fredhutch.org: 1 yahoo.de: 1 sph.cuny.edu: 1 bsse.ethz.ch: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 3
  • Total pull requests: 2
  • Average time to close issues: 14 days
  • Average time to close pull requests: less than a minute
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • MartinFXP (3)
Pull Request Authors
  • MartinFXP (2)
Top Labels
Issue Labels
bug (3) enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 17,199 total
  • Total dependent packages: 4
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: epiNEM

epiNEM

  • Versions: 5
  • Dependent Packages: 4
  • Dependent Repositories: 0
  • Downloads: 17,199 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 19.2%
Downloads: 57.5%
Maintainers (1)
martinpirkl@yahoo.de
Last synced: 10 months ago